Each area of the body dissipates heat at different rates in order to keep a constant temperature. This is because the enzymes in your body (that catalyse with other substances to create everything your body needs to go on) are very sensitive to temperature (which is the quantum movements of atoms). Your head and body may not be the same temperature externally but that is because they are regulating your internal body temperature to keep a core constant.
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I think this is to do with circulation to your hands and feet as you move them a lot. This extra blood causes the warmth.